mvallieres / Radiomics

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|https://github.com/mvallieres/radiomics/| --> A package providing MATLAB programming tools for radiomics analysis.

REFERENCES: [1] Vallières, M. et al. (2015). A radiomics model from joint FDG-PET and MRI texture features for the prediction of lung metastases in soft-tissue sarcomas of the extremities. Physics in Medicine and Biology, 60(14), 5471-5496. doi:10.1088/0031-9155/60/14/5471

[2] Zhou, H., Vallières, M., Bai, H.X. et al. (2017). MRI features predict survival and molecular markers in diffuse lower-grade gliomas.
Neuro-Oncology, 19(6), 862-870. doi:10.1093/neuonc/now256

[3] Vallière, M. et al. (2017). Radiomics strategies for risk assessment
of tumour failure in head-and-neck cancer. Scientific Reports, 7:10117. doi:10.1038/s41598-017-10371-5

AUTHOR: Martin Vallières [email protected]

HISTORY:

• Version 1.0: May 2015

DISCLAIMER: "I'm not a programmer, I'm just a scientist doing stuff!"

*** THANK YOU FOR YOUR INTEREST IN THIS PACKAGE *** --> If you have any questions, comments or suggestions about this package, please do not hesitate to contact me!

This package contains 5 folders:

1. 'TextureToolbox': MATLAB codes to perform texture analysis from an input 2D or 3D region of interest (ROI). This toolbox is self-contained and can be used on its own outside of the radiomics package. In particular, this texture analysis package implements wavelet band-pass filtering, isotropic resampling, discretization length corrections and different quantization tools. Please see ref. [1] for more details.

2. 'NonTextureFeatures': MATLAB codes to compute features other than textures from an input 3D region of interest (ROI). Include features such as SUV metrics, AUC-CSH, Percent Inactive, Size, Solidity, Volume and Eccentricity. Please see ref. [1] for more details.

3. 'MultivariableModeling': MATLAB codes to perform multivariable analysis operations such as logistic regression, bootstrapping, feature set reduction, feature set selection, prediction performance estimation, etc.

4. 'Utilities': MATLAB codes used to perform different operations including the computation of SUV maps, reading of directory containing DICOM imaging data, conversion of RTstruct DICOM objects to 3D masks, etc.

5. 'STUDIES': MATLAB codes used for specific studies. To reproduce the experiments of a given study, please see its corresponding folder.

   • 'STS_study': Ref. [1] A. Imaging/ROI data and clinical information is available on The Cancer Imaging Archive (TCIA) website under the following DOI: http://dx.doi.org/10.7937/K9/TCIA.2015.7GO2GSKS.
   • 'LGG_study': Ref. [2] A. Texture data ("TEXTURES_TCGA.zip") is available on Google Drive: https://drive.google.com/open?id=0B0fcZCGXT3nZWXM5d0t3OXVjQzA B. Imaging data is available on the TCIA website: http://doi.org/10.7937/K9/TCIA.2016.L4LTD3TK C. ROI data is available on the TCIA website: https://doi.org/10.7937/K9/TCIA.2017.BD7SGWCA
   • 'HN_study': Ref. [3] A. Imaging/ROI data and clinical information is available on the TCIA website: http://doi.org/10.7937/K9/TCIA.2017.8oje5q00

ACKNOWLEDGEMENTS: other software code

• Wei's GLRLM toolbox: Xunkai Wei, Gray Level Run Length Matrix Toolbox v1.0, Software,Beijing Aeronautical Technology Research Center, 2007. http://www.mathworks.com/matlabcentral/fileexchange/17482-gray-level-run-length-matrix-toolbox
• Q. Li: http://www.mathworks.com/matlabcentral/fileexchange/23377-ellipsoid-fitting
• CERR development team: http://www.cerr.info/
• Dirk-Jan Kroon (imresize3D.m): http://www.mathworks.com/matlabcentral/fileexchange/21451-multimodality-non-rigid-demon-algorithm-image-registration/content//functions/imresize3d.m
• David Reshef and Yakir Reshef: MINE version 1.0.1d http://www.exploredata.net/
• DREES development team: http://www.cerr.info/drees
• Enric Junqué de Fortuny (fastAUC.cpp): http://www.mathworks.com/matlabcentral/fileexchange/41258-faster-roc-auc
• François Beauducel (roundsd.m): http://www.mathworks.com/matlabcentral/fileexchange/26212-round-with-significant-digits
• Jos van der Geest (herrorbar.m): http://www.mathworks.com/matlabcentral/fileexchange/3963-herrorbar